Open bh-lyu opened 2 years ago
When you created the FreeSurfer directories, did you pass -T2 /path/to/T2w.nii.gz
? It seems that that step is missing.
You should be able to correct with:
recon-all -s sub-CCNP020 -T2 $bidsDir/sub-CCNP020/*/anat/sub-CCNP020_*T2w.nii.gz
What happened?
I am running a large 100 subjects data set and found a few subjects failed and reporting the error. I reran one the of the failed subjects ('sub-CCNP020') and reported the same error in the log shown below.
It seems the report was related to the T2raw.mgz. But I checked the original T2 image and the image was normal as other successful subjects.
What command did you use?
What version of fMRIPrep are you running?
20.2.5
How are you running fMRIPrep?
Docker
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
FreeSurfer
Please copy and paste any relevant log output.
Additional information / screenshots
No response